6eri
From Proteopedia
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| - | '''Unreleased structure''' | ||
| - | + | ==Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor== | |
| + | <SX load='6eri' size='340' side='right' viewer='molstar' caption='[[6eri]], [[Resolution|resolution]] 3.00Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6eri]] is a 57 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ERI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ERI FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
| + | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6eri FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eri OCA], [http://pdbe.org/6eri PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eri RCSB], [http://www.ebi.ac.uk/pdbsum/6eri PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eri ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [[http://www.uniprot.org/uniprot/RRFC_SPIOL RRFC_SPIOL]] Responsible for the release of ribosomes from messenger RNA at the termination of chloroplastic protein biosynthesis. [[http://www.uniprot.org/uniprot/RK27_SPIOL RK27_SPIOL]] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.<ref>PMID:10874046</ref> <ref>PMID:28007896</ref> [[http://www.uniprot.org/uniprot/RK6_SPIOL RK6_SPIOL]] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.<ref>PMID:10874046</ref> <ref>PMID:28007896</ref> [[http://www.uniprot.org/uniprot/RK21_SPIOL RK21_SPIOL]] This protein binds to 23S ribosomal RNA in the presence of protein L20 (By similarity). [[http://www.uniprot.org/uniprot/RK22_SPIOL RK22_SPIOL]] This protein binds specifically to 23S rRNA (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity). Binds an erythromycin derivative added to the 50S subunit. [[http://www.uniprot.org/uniprot/RK20_SPIOL RK20_SPIOL]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity).[HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/PRSP1_SPIOL PRSP1_SPIOL]] A ribosome-binding factor that may be involved in an unknown stress response. Modeling onto the 70S spinach chloroplast ribosome and its position in the E.coli 70S ribosome suggests it binds in the decoding region of the 30S ribosomal subunit, precluding the binding of tRNA to the ribosome. Its position is incompatible with translation. Upon expression in E.coli binds to 30S and 70S ribosomes, decreases binding of tRNA(fMet). Stabilizes 70S ribosomes against dissociation. May be recycled by the combined action of ribosome-recycling factor (RRF) and EF-G.<ref>PMID:19965869</ref> [[http://www.uniprot.org/uniprot/RK34_SPIOL RK34_SPIOL]] This protein binds directly to 23S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RR7_SPIOL RR7_SPIOL]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit (By similarity).[HAMAP-Rule:MF_00480] [[http://www.uniprot.org/uniprot/RK18_SPIOL RK18_SPIOL]] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.<ref>PMID:10874046</ref> <ref>PMID:28007896</ref> [[http://www.uniprot.org/uniprot/RK24_SPIOL RK24_SPIOL]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity). Located at the polypeptide exit tunnel on the outside of the subunit. [[http://www.uniprot.org/uniprot/RK31_SPIOL RK31_SPIOL]] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.<ref>PMID:10874046</ref> <ref>PMID:28007896</ref> [[http://www.uniprot.org/uniprot/RK14_SPIOL RK14_SPIOL]] Binds to 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/RK15_SPIOL RK15_SPIOL]] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.<ref>PMID:10874046</ref> <ref>PMID:28007896</ref> [[http://www.uniprot.org/uniprot/RR20_SPIOL RR20_SPIOL]] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.<ref>PMID:10874039</ref> <ref>PMID:28007896</ref> [[http://www.uniprot.org/uniprot/RR9_SPIOL RR9_SPIOL]] Binds directly to 16S ribosomal RNA.<ref>PMID:10874039</ref> [:] [[http://www.uniprot.org/uniprot/RK28_SPIOL RK28_SPIOL]] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.<ref>PMID:10874046</ref> <ref>PMID:28007896</ref> [[http://www.uniprot.org/uniprot/RR13_SPIOL RR13_SPIOL]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/RK17_SPIOL RK17_SPIOL]] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.<ref>PMID:10874046</ref> <ref>PMID:28007896</ref> [[http://www.uniprot.org/uniprot/RK29_SPIOL RK29_SPIOL]] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.<ref>PMID:10874046</ref> <ref>PMID:28007896</ref> [[http://www.uniprot.org/uniprot/RK5_SPIOL RK5_SPIOL]] Binds 5S rRNA, forms part of the central protuberance of the 50S subunit (By similarity). [[http://www.uniprot.org/uniprot/RR17_SPIOL RR17_SPIOL]] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.<ref>PMID:10874039</ref> <ref>PMID:28007896</ref> [[http://www.uniprot.org/uniprot/RR6_SPIOL RR6_SPIOL]] Binds together with S18 to 16S ribosomal RNA (By similarity).[UniProtKB:O78447] [[http://www.uniprot.org/uniprot/RR8_SPIOL RR8_SPIOL]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_01302] [[http://www.uniprot.org/uniprot/RR14_SPIOL RR14_SPIOL]] Binds 16S rRNA, required for the assembly of 30S particles (By similarity).[:] [[http://www.uniprot.org/uniprot/RK19_SPIOL RK19_SPIOL]] Located at the 30S-50S ribosomal subunit interface and binds directly to 23S ribosomal RNA (By similarity).[:] [[http://www.uniprot.org/uniprot/RK9_SPIOL RK9_SPIOL]] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.<ref>PMID:10874046</ref> <ref>PMID:28007896</ref> [[http://www.uniprot.org/uniprot/RR19_SPIOL RR19_SPIOL]] This protein binds directly to 16S ribosomal RNA.<ref>PMID:10874039</ref> [[http://www.uniprot.org/uniprot/RR5_SPIOL RR5_SPIOL]] Binds directly to 16S ribosomal RNA. Involved in spectinomycin and neamine resistance and streptomycin independence.[:] [[http://www.uniprot.org/uniprot/RK3_SPIOL RK3_SPIOL]] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.<ref>PMID:10874046</ref> <ref>PMID:28007896</ref> [[http://www.uniprot.org/uniprot/RR12_SPIOL RR12_SPIOL]] With S4 and S5 plays an important role in translational accuracy. Located at the interface of the 30S and 50S subunits (By similarity).[HAMAP-Rule:MF_00403_B] [[http://www.uniprot.org/uniprot/RR4_SPIOL RR4_SPIOL]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit (By similarity).[HAMAP-Rule:MF_01306] With S5 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01306] [[http://www.uniprot.org/uniprot/RR10_SPIOL RR10_SPIOL]] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.<ref>PMID:10874039</ref> <ref>PMID:28007896</ref> [[http://www.uniprot.org/uniprot/RK23_SPIOL RK23_SPIOL]] Binds to 23S rRNA (By similarity). Located at the polypeptide exit tunnel on the outside of the subunit. [[http://www.uniprot.org/uniprot/RR21_SPIOL RR21_SPIOL]] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.<ref>PMID:10874039</ref> <ref>PMID:28007896</ref> [[http://www.uniprot.org/uniprot/RK4_SPIOL RK4_SPIOL]] Probably binds the 23S rRNA (By similarity). This protein (expressed without the transit peptide) is able to provoke transcription termination from the spinach chloroplast rDNA operon and the E.coli S10 operon in vitro. | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions underpinning this process in plants take place in the chloroplast. Chloroplasts evolved ~1.2 billion years ago from an engulfed primordial diazotrophic cyanobacterium, and chlororibosomes are responsible for synthesis of the core proteins driving photochemical reactions. Chlororibosomal activity is spatiotemporally coupled to the synthesis and incorporation of functionally essential co-factors, implying the presence of chloroplast-specific regulatory mechanisms and structural adaptation of the chlororibosome(1,2). Despite recent structural information(3-6), some of these aspects remained elusive. To provide new insights into the structural specialities and evolution, we report a comprehensive analysis of the 2.9-3.1 A resolution electron cryo-microscopy structure of the spinach chlororibosome in complex with its recycling factor and hibernation-promoting factor. The model reveals a prominent channel extending from the exit tunnel to the chlororibosome exterior, structural re-arrangements that lead to increased surface area for translocon binding, and experimental evidence for parallel and convergent evolution of chloro- and mitoribosomes. | ||
| - | + | Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor.,Boerema AP, Aibara S, Paul B, Tobiasson V, Kimanius D, Forsberg BO, Wallden K, Lindahl E, Amunts A Nat Plants. 2018 Apr;4(4):212-217. doi: 10.1038/s41477-018-0129-6. Epub 2018 Apr , 2. PMID:29610536<ref>PMID:29610536</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 6eri" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Ribosome 3D structures|Ribosome 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </SX> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Spinacia oleracea]] | ||
| + | [[Category: Aibara, S]] | ||
| + | [[Category: Amunts, A]] | ||
| + | [[Category: Borema, A Perez]] | ||
| + | [[Category: Forsberg, B O]] | ||
| + | [[Category: Kimanius, D]] | ||
| + | [[Category: Lindahl, E]] | ||
| + | [[Category: Paul, B]] | ||
| + | [[Category: Tobiasson, V]] | ||
| + | [[Category: Wallden, K]] | ||
| + | [[Category: Chloroplast]] | ||
| + | [[Category: Ribosome]] | ||
| + | [[Category: Translation]] | ||
Current revision
Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor
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